Two thoughts:
1) top is the wrong tool to monitor overall physical memory consumption. It reports user space consumption/status only. (Hence why the Real [actual RAM] in use doesn't match the actual physical memory on the box in most cases -- first, the system will always need some for itself and second, most times you look you aren't at 100% utilization anyway). Don't blame the native top for not reporting what you want -- it isn't intended to do so. Other tools (such as Glance as mentioned) are better suited if you want to monitor overall RAM usage on the system.
2) Whatever GNU top is doing, it sure looks to me like it is trying to use /dev/kmem to go peeking through the kernel internals with some assumptions as to data structures. In your case, it certainly appears said assumptions are wrong. [This is why binaries which assume /dev/kmem is safe to go tromping through are inherently risky for compatibility.] Since you can't force a new kernel to be built with whatever GNU top is expecting, I doubt this ERROR is going away.
